Whether the interface is balanced (IEC 60958 Type I using XLR) or not (IEC 60958 Type II using RCA/coax) is of no importance to the symptoms. Both interfaces carry computer generated SPDIF-signals with all problems related to it. Those subtle problems in sound quality are inherent to the SPDIF-signal, and exist even when there is proper signal transfer without coarse issues like grounding loops, signal decay and/or dropped packets.
The latter problems could benefit from dedicated sound hardware inside the PC coupled to balanced connections. On the other hand, if you experience those issues at your home setup, something else is wrong. They are intended for professional use where long distances between devices are required and the prevention of electrical problems (in the rest of the delivery chain) is more important than sound quality. That's also the reason that currently not a single professional audio device exists which aims at bit-perfectness in the whole chain.